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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / refman.idx

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+\indexentry{R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding@{R\discretionary {-}{}{}N\discretionary {-}{}{}A Secondary Structure Folding}|hyperpage}{19}
+\indexentry{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}|hyperpage}{22}
+\indexentry{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}!fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{23}
+\indexentry{fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}|hyperpage}{23}
+\indexentry{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}!fold@{fold}|hyperpage}{23}
+\indexentry{fold@{fold}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}|hyperpage}{23}
+\indexentry{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}!circfold@{circfold}|hyperpage}{24}
+\indexentry{circfold@{circfold}!Calculating Minimum Free Energy (MFE) Structures@{Calculating Minimum Free Energy (\discretionary {-}{}{}M\discretionary {-}{}{}F\discretionary {-}{}{}E) Structures}|hyperpage}{24}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{25}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{26}
+\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{26}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{27}
+\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{27}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{28}
+\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}circ\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{28}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{29}
+\indexentry{free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{free\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{29}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}|hyperpage}{29}
+\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{29}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}|hyperpage}{29}
+\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{29}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}|hyperpage}{29}
+\indexentry{assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{assign\discretionary {-}{}{}\_\discretionary {-}{}{}plist\discretionary {-}{}{}\_\discretionary {-}{}{}from\discretionary {-}{}{}\_\discretionary {-}{}{}pr}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{29}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{30}
+\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{get\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{30}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}|hyperpage}{30}
+\indexentry{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{30}
+\indexentry{Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}!mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}|hyperpage}{31}
+\indexentry{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{mean\discretionary {-}{}{}\_\discretionary {-}{}{}bp\discretionary {-}{}{}\_\discretionary {-}{}{}distance\discretionary {-}{}{}\_\discretionary {-}{}{}pr}!Calculating Partition Functions and Pair Probabilities@{Calculating Partition Functions and Pair Probabilities}|hyperpage}{31}
+\indexentry{Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)@{Compute the structure with maximum expected accuracy (\discretionary {-}{}{}M\discretionary {-}{}{}E\discretionary {-}{}{}A)}|hyperpage}{32}
+\indexentry{Compute the centroid structure@{Compute the centroid structure}|hyperpage}{33}
+\indexentry{Compute the centroid structure@{Compute the centroid structure}!get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}|hyperpage}{33}
+\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pl}!Compute the centroid structure@{Compute the centroid structure}|hyperpage}{33}
+\indexentry{Compute the centroid structure@{Compute the centroid structure}!get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}|hyperpage}{33}
+\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr@{get\discretionary {-}{}{}\_\discretionary {-}{}{}centroid\discretionary {-}{}{}\_\discretionary {-}{}{}struct\discretionary {-}{}{}\_\discretionary {-}{}{}pr}!Compute the centroid structure@{Compute the centroid structure}|hyperpage}{33}
+\indexentry{Enumerating Suboptimal Structures@{Enumerating Suboptimal Structures}|hyperpage}{35}
+\indexentry{Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}|hyperpage}{36}
+\indexentry{Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}!zukersubopt@{zukersubopt}|hyperpage}{36}
+\indexentry{zukersubopt@{zukersubopt}!Suboptimal structures according to Zuker et al. 1989@{Suboptimal structures according to Zuker et al. 1989}|hyperpage}{36}
+\indexentry{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{37}
+\indexentry{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}!subopt@{subopt}|hyperpage}{37}
+\indexentry{subopt@{subopt}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{37}
+\indexentry{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}!subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}|hyperpage}{38}
+\indexentry{subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{subopt\discretionary {-}{}{}\_\discretionary {-}{}{}circ}!Suboptimal structures within an energy band arround the MFE@{Suboptimal structures within an energy band arround the M\discretionary {-}{}{}F\discretionary {-}{}{}E}|hyperpage}{38}
+\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{39}
+\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack@{pbacktrack}|hyperpage}{39}
+\indexentry{pbacktrack@{pbacktrack}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{39}
+\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}|hyperpage}{40}
+\indexentry{pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ@{pbacktrack\discretionary {-}{}{}\_\discretionary {-}{}{}circ}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{40}
+\indexentry{Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}!st\discretionary {-}{}{}\_\discretionary {-}{}{}back@{st\discretionary {-}{}{}\_\discretionary {-}{}{}back}|hyperpage}{40}
+\indexentry{st\discretionary {-}{}{}\_\discretionary {-}{}{}back@{st\discretionary {-}{}{}\_\discretionary {-}{}{}back}!Stochastic backtracking in the Ensemble@{Stochastic backtracking in the Ensemble}|hyperpage}{40}
+\indexentry{Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization@{Calculate Secondary Structures of two R\discretionary {-}{}{}N\discretionary {-}{}{}As upon Dimerization}|hyperpage}{41}
+\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{42}
+\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}!cofold@{cofold}|hyperpage}{42}
+\indexentry{cofold@{cofold}!MFE Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{42}
+\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}!export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}|hyperpage}{43}
+\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays\discretionary {-}{}{}\_\discretionary {-}{}{}gq}!MFE Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{43}
+\indexentry{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}!export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{43}
+\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{export\discretionary {-}{}{}\_\discretionary {-}{}{}cofold\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}!MFE Structures of two hybridized Sequences@{M\discretionary {-}{}{}F\discretionary {-}{}{}E Structures of two hybridized Sequences}|hyperpage}{43}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{44}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}|hyperpage}{45}
+\indexentry{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{45}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{45}
+\indexentry{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par@{co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}fold\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{45}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}|hyperpage}{46}
+\indexentry{export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm@{export\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}bppm}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{46}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}|hyperpage}{46}
+\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{46}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}|hyperpage}{46}
+\indexentry{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par@{update\discretionary {-}{}{}\_\discretionary {-}{}{}co\discretionary {-}{}{}\_\discretionary {-}{}{}pf\discretionary {-}{}{}\_\discretionary {-}{}{}params\discretionary {-}{}{}\_\discretionary {-}{}{}par}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{46}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities@{compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}|hyperpage}{47}
+\indexentry{compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities@{compute\discretionary {-}{}{}\_\discretionary {-}{}{}probabilities}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{47}
+\indexentry{Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}!get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations@{get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}|hyperpage}{47}
+\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations@{get\discretionary {-}{}{}\_\discretionary {-}{}{}concentrations}!Partition Function for two hybridized Sequences@{Partition Function for two hybridized Sequences}|hyperpage}{47}
+\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{48}
+\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}|hyperpage}{48}
+\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}unstru}!Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{48}
+\indexentry{Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}!pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}|hyperpage}{49}
+\indexentry{pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact@{pf\discretionary {-}{}{}\_\discretionary {-}{}{}interact}!Partition Function for two hybridized Sequences as a stepwise Process@{Partition Function for two hybridized Sequences as a stepwise Process}|hyperpage}{49}
+\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{50}
+\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi@{get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}|hyperpage}{51}
+\indexentry{get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi@{get\discretionary {-}{}{}\_\discretionary {-}{}{}mpi}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{51}
+\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}|hyperpage}{51}
+\indexentry{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct@{energy\discretionary {-}{}{}\_\discretionary {-}{}{}of\discretionary {-}{}{}\_\discretionary {-}{}{}alistruct}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}|hyperpage}{51}
+\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence@{encode\discretionary {-}{}{}\_\discretionary {-}{}{}ali\discretionary {-}{}{}\_\discretionary {-}{}{}sequence}|hyperpage}{51}
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+\indexentry{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays@{alloc\discretionary {-}{}{}\_\discretionary {-}{}{}sequence\discretionary {-}{}{}\_\discretionary {-}{}{}arrays}|hyperpage}{52}
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+\indexentry{Classified Dynamic Programming@{Classified Dynamic Programming}|hyperpage}{79}
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+\indexentry{Compute the Density of States@{Compute the Density of States}|hyperpage}{89}
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